diff --git a/easybuild/easyconfigs/p/psmc/psmc-0.6.5_20221121-GCC-12.3.0.eb b/easybuild/easyconfigs/p/psmc/psmc-0.6.5_20221121-GCC-12.3.0.eb new file mode 100644 index 00000000000..d59f8ed5d78 --- /dev/null +++ b/easybuild/easyconfigs/p/psmc/psmc-0.6.5_20221121-GCC-12.3.0.eb @@ -0,0 +1,54 @@ +easyblock = 'MakeCp' + +name = 'psmc' +version = '0.6.5_20221121' +_commit = '8bd902f' + +homepage = 'https://github.com/lh3/psmc' +description = """This software package infers population size history from a diploid sequence +using the Pairwise Sequentially Markovian Coalescent (PSMC) model.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/lh3/psmc/archive/'] +sources = [{ + 'source_urls': ['https://github.com/lh3/psmc/archive/'], + 'download_filename': '%s.tar.gz' % _commit, + 'filename': SOURCE_TAR_GZ, +}] +checksums = ['24a79addd863d91c7f19bcd2dc2cb16bb3d7b303d5ff44e48b8b89c975cf1c49'] + +dependencies = [('Perl', '5.36.1')] + +buildopts = '&& cd utils && make' + +local_utils = [ + 'avg.pl', 'calD', 'cntcpg', 'ctime_plot.pl', 'dec2ctime.pl', 'decode2bed.pl', 'fq2psmcfa', 'history2ms.pl', + 'ms2psmcfa.pl', 'mutDiff', 'pcnt_bezier.lua', 'psmc2history.pl', 'psmc_plot.pl', 'psmc_trunc.pl', 'splitfa', +] + +files_to_copy = [ + (['psmc'], 'bin'), + (['utils/%s' % x for x in local_utils], 'bin') +] + +postinstallcmds = [ + # recommended help, see perldoc Getopt::Std + "sed -i '/use Getopt::Std;/a $Getopt::Std::STANDARD_HELP_VERSION = 1;' %(installdir)s/bin/*.pl", +] + +fix_perl_shebang_for = ['bin/*.pl'] + +sanity_check_paths = { + 'files': ['bin/psmc'] + ['bin/%s' % x for x in local_utils], + 'dirs': [], +} + +sanity_check_commands = [ + 'psmc 2>&1 |grep "Usage:"', + 'calD 2>&1 |grep "Usage:"', + 'avg.pl --help', + 'ctime_plot.pl --help', +] + +moduleclass = 'bio'